def make_calpha_arrow_mesh(trace, length=0.7, width=0.35, thickness=0.3):
arrow = render.Arrow(length, width, thickness)
n_point = len(trace.points)
triangle_store = TriangleStore(n_point * len(arrow.indices))
for i_point in range(n_point):
orientate = arrow.get_orientate(trace.tangents[i_point],
trace.ups[i_point], 1.0)
for indices in group(arrow.indices, 3):
points = [arrow.vertices[i] for i in indices]
normal = v3.cross(points[1] - points[0], points[0] - points[2])
normal = v3.transform(orientate, normal)
for point in points:
triangle_store.add_vertex(
v3.transform(orientate, point) + trace.points[i_point],
normal, trace.residues[i_point].color,
trace.objids[i_point])
return triangle_store.vertex_buffer()
def make_cylinder_trace_mesh(pieces, coil_detail=4, radius=0.3):
cylinder = render.Cylinder(coil_detail)
n_point = sum(len(piece.points) for piece in pieces)
triangle_store = TriangleStore(2 * n_point * cylinder.n_vertex)
for piece in pieces:
points = piece.points
for i_point in xrange(len(points) - 1):
tangent = 0.5 * (points[i_point + 1] - points[i_point])
up = piece.ups[i_point] + piece.ups[i_point + 1]
orientate = cylinder.get_orientate(tangent, up, radius)
triangle_store.setup_next_strip(cylinder.indices)
for point, normal in zip(cylinder.points, cylinder.normals):
triangle_store.add_vertex(
v3.transform(orientate, point) + points[i_point],
v3.transform(orientate, normal),
piece.residues[i_point].color, piece.objids[i_point])
orientate = cylinder.get_orientate(-tangent, up, radius)
triangle_store.setup_next_strip(cylinder.indices)
for point, normal in zip(cylinder.points, cylinder.normals):
triangle_store.add_vertex(
v3.transform(orientate, point) + points[i_point + 1],
v3.transform(orientate,
normal), piece.residues[i_point + 1].color,
piece.objids[i_point + 1])
return triangle_store.index_buffer(), triangle_store.vertex_buffer()
def make_cylinder_trace_mesh(pieces, coil_detail=4, radius=0.3):
cylinder = render.Cylinder(coil_detail)
n_point = sum(len(piece.points) for piece in pieces)
triangle_store = TriangleStore(2 * n_point * cylinder.n_vertex)
for piece in pieces:
points = piece.points
for i_point in xrange(len(points) - 1):
tangent = 0.5*(points[i_point+1] - points[i_point])
up = piece.ups[i_point] + piece.ups[i_point+1]
orientate = cylinder.get_orientate(tangent, up, radius)
triangle_store.setup_next_strip(cylinder.indices)
for point, normal in zip(cylinder.points, cylinder.normals):
triangle_store.add_vertex(
v3.transform(orientate, point) + points[i_point],
v3.transform(orientate, normal),
piece.residues[i_point].color,
piece.objids[i_point])
orientate = cylinder.get_orientate(-tangent, up, radius)
triangle_store.setup_next_strip(cylinder.indices)
for point, normal in zip(cylinder.points, cylinder.normals):
triangle_store.add_vertex(
v3.transform(orientate, point) + points[i_point+1],
v3.transform(orientate, normal),
piece.residues[i_point+1].color,
piece.objids[i_point+1])
return triangle_store.index_buffer(), triangle_store.vertex_buffer()
def make_calpha_arrow_mesh(
trace, length=0.7, width=0.35, thickness=0.3):
arrow = render.Arrow(length, width, thickness)
n_point = len(trace.points)
triangle_store = TriangleStore(n_point*len(arrow.indices))
for i_point in range(n_point):
orientate = arrow.get_orientate(
trace.tangents[i_point], trace.ups[i_point], 1.0)
for indices in group(arrow.indices, 3):
points = [arrow.vertices[i] for i in indices]
normal = v3.cross(points[1] - points[0], points[0] - points[2])
normal = v3.transform(orientate, normal)
for point in points:
triangle_store.add_vertex(
v3.transform(orientate, point) + trace.points[i_point],
normal,
trace.residues[i_point].color,
trace.objids[i_point])
return triangle_store.vertex_buffer()
def make_ball_and_stick_mesh(
rendered_soup, sphere_stack=5, sphere_arc=5,
tube_arc=5, radius=0.2):
sphere = render.Sphere(sphere_stack, sphere_arc)
cylinder = render.Cylinder(4)
n_vertex = len(rendered_soup.draw_to_screen_atoms)*sphere.n_vertex
n_vertex += len(rendered_soup.bonds)*cylinder.n_vertex
triangle_store = render.TriangleStore(n_vertex)
for atom in rendered_soup.draw_to_screen_atoms:
triangle_store.setup_next_strip(sphere.indices)
orientate = sphere.get_orientate(radius)
for point in sphere.points:
triangle_store.add_vertex(
v3.transform(orientate, point) + atom.pos,
point, # same as normal!
atom.residue.color,
atom.residue.objid)
for bond in rendered_soup.bonds:
orientate = cylinder.get_orientate(bond.tangent, bond.up, radius)
triangle_store.setup_next_strip(cylinder.indices)
for point, normal in zip(cylinder.points, cylinder.normals):
triangle_store.add_vertex(
v3.transform(orientate, point) + bond.atom1.pos,
v3.transform(orientate, normal),
bond.atom1.residue.color,
bond.atom1.residue.objid)
return triangle_store.index_buffer(), triangle_store.vertex_buffer()
def test_matrix_combination():
n = 4
x = v3.random_vector()
y1 = v3.vector(x)
matrix = v3.identity()
for i in range(4):
r_matrix = v3.random_matrix()
y1 = v3.transform(r_matrix, y1)
matrix = v3.combine(r_matrix, matrix)
y2 = v3.transform(matrix, x)
assert v3.is_similar_vector(y1, y2)
def test_matrix_combination():
n = 4
x = v3.random_vector()
y1 = v3.vector(x)
matrix = v3.identity()
for i in range(4):
r_matrix = v3.random_matrix()
y1 = v3.transform(r_matrix, y1)
matrix = v3.combine(r_matrix, matrix)
y2 = v3.transform(matrix, x)
assert v3.is_similar_vector(y1, y2)
def test_orthogonality(): x = v3.vector(v3.random_mag(), 0, 0) y = v3.vector(0, v3.random_mag(), 0) z = v3.vector(0, 0, v3.random_mag()) ry_x = v3.transform(v3.rotation(y, v3.radians(90)), x) assert v3.is_similar_vector(v3.norm(ry_x), -v3.norm(z)) assert v3.is_similar_mag(v3.mag(ry_x), v3.mag(x)) ry_z = v3.transform(v3.rotation(y, v3.radians(90)), z) assert v3.is_similar_vector(v3.norm(ry_z), v3.norm(x)) cross_x_y = v3.cross(x, y) assert v3.is_similar_vector(v3.norm(cross_x_y), v3.norm(z)) cross_y_x = v3.cross(y, x) assert v3.is_similar_vector(v3.norm(cross_y_x), -v3.norm(z))
def test_orthogonality():
x = v3.vector(v3.random_mag(), 0, 0)
y = v3.vector(0, v3.random_mag(), 0)
z = v3.vector(0, 0, v3.random_mag())
ry_x = v3.transform(v3.rotation(y, v3.radians(90)), x)
assert v3.is_similar_vector(v3.norm(ry_x), -v3.norm(z))
assert v3.is_similar_mag(v3.mag(ry_x), v3.mag(x))
ry_z = v3.transform(v3.rotation(y, v3.radians(90)), z)
assert v3.is_similar_vector(v3.norm(ry_z), v3.norm(x))
cross_x_y = v3.cross(x, y)
assert v3.is_similar_vector(v3.norm(cross_x_y), v3.norm(z))
cross_y_x = v3.cross(y, x)
assert v3.is_similar_vector(v3.norm(cross_y_x), -v3.norm(z))
def make_ball_and_stick_mesh(rendered_soup,
sphere_stack=5,
sphere_arc=5,
tube_arc=5,
radius=0.2):
sphere = render.Sphere(sphere_stack, sphere_arc)
cylinder = render.Cylinder(4)
n_vertex = len(rendered_soup.draw_to_screen_atoms) * sphere.n_vertex
n_vertex += 2 * len(rendered_soup.bonds) * cylinder.n_vertex
triangle_store = TriangleStore(n_vertex)
for atom in rendered_soup.draw_to_screen_atoms:
triangle_store.setup_next_strip(sphere.indices)
orientate = sphere.get_orientate(radius)
for point in sphere.points:
triangle_store.add_vertex(
v3.transform(orientate, point) + atom.pos,
point, # same as normal!
atom.residue.color,
atom.objid)
for bond in rendered_soup.bonds:
tangent = 0.5 * bond.tangent
orientate = cylinder.get_orientate(tangent, bond.up, radius)
triangle_store.setup_next_strip(cylinder.indices)
for point, normal in zip(cylinder.points, cylinder.normals):
triangle_store.add_vertex(
v3.transform(orientate, point) + bond.atom1.pos,
v3.transform(orientate, normal), bond.atom1.residue.color,
bond.atom1.objid)
orientate = cylinder.get_orientate(-tangent, bond.up, radius)
triangle_store.setup_next_strip(cylinder.indices)
for point, normal in zip(cylinder.points, cylinder.normals):
triangle_store.add_vertex(
v3.transform(orientate, point) + bond.atom2.pos,
v3.transform(orientate, normal), bond.atom2.residue.color,
bond.atom2.objid)
return triangle_store.index_buffer(), triangle_store.vertex_buffer()
def __init__(self, n_arc=10, radius=1.0):
self.n_arc = n_arc
tangent = v3.vector(0, 0, 1)
rotator = v3.vector(0, radius, 0)
self.arcs = []
angle = v3.radians(360 / n_arc)
rotation = v3.rotation(tangent, angle)
self.arcs.append(v3.vector(rotator))
for i_segment in range(n_arc - 1):
rotator = v3.transform(rotation, rotator)
self.arcs.append(rotator)
self.normals = calc_cyclic_normals(self.arcs, tangent)
def test_rotation(): x = v3.random_vector() y = v3.transform(v3.random_rotation(), x) assert v3.is_similar_mag(v3.mag(x), v3.mag(y))
def test_translation(): x = v3.vector(v3.random_mag(), 0, 0) y = v3.vector(0, v3.random_mag(), 0) x_and_y = v3.transform(v3.translation(y), x) assert v3.is_similar_vector(x_and_y, x+y)
def test_rotation():
x = v3.random_vector()
y = v3.transform(v3.random_rotation(), x)
assert v3.is_similar_mag(v3.mag(x), v3.mag(y))
def test_translation():
x = v3.vector(v3.random_mag(), 0, 0)
y = v3.vector(0, v3.random_mag(), 0)
x_and_y = v3.transform(v3.translation(y), x)
assert v3.is_similar_vector(x_and_y, x + y)
def build_triangles(self, vertex_buffer):
n_point = len(self.trace.points)
n_arc = len(self.profile.arcs)
# draw front face
indices = []
for i_arc in range((n_arc - 1) / 2):
indices.extend([i_arc, i_arc + 1, n_arc - 1 - i_arc])
indices.extend([n_arc - 1 - i_arc, i_arc + 1, n_arc - 2 - i_arc])
vertex_buffer.setup_next_strip(indices)
m = get_xy_face_transform(self.trace.tangents[0], self.trace.ups[0],
1.0)
arcs = [
v3.transform(m, a) + self.trace.points[0]
for a in self.profile.arcs
]
normal = -self.trace.tangents[0]
for i_arc in range(n_arc):
vertex_buffer.add_vertex(arcs[i_arc], normal, self.color,
self.trace.objids[0])
# draw extrusion in tube
indices = []
for i_point in range(n_point - 1):
i_slice_offset = i_point * n_arc
j_slice_offset = (i_point + 1) * n_arc
for i_arc in range(n_arc):
j_arc = (i_arc + 1) % n_arc
indices.append(i_slice_offset + i_arc)
indices.append(j_slice_offset + i_arc)
indices.append(i_slice_offset + j_arc)
indices.append(i_slice_offset + j_arc)
indices.append(j_slice_offset + i_arc)
indices.append(j_slice_offset + j_arc)
vertex_buffer.setup_next_strip(indices)
for i in range(n_point):
m = get_xy_face_transform(self.trace.tangents[i],
self.trace.ups[i], 1.0)
arcs = [
v3.transform(m, a) + self.trace.points[i]
for a in self.profile.arcs
]
normals = [v3.transform(m, n) for n in self.profile.normals]
for i_arc in range(n_arc):
vertex_buffer.add_vertex(arcs[i_arc], normals[i_arc],
self.color, self.trace.objids[i])
# draw back face
indices = []
for i_arc in range((n_arc - 1) / 2):
indices.extend([i_arc, i_arc + 1, n_arc - 1 - i_arc])
indices.extend([n_arc - 1 - i_arc, i_arc + 1, n_arc - 2 - i_arc])
vertex_buffer.setup_next_strip(indices)
i_point = n_point - 1
m = get_xy_face_transform(self.trace.tangents[i_point],
self.trace.ups[i_point], 1.0)
arcs = [
v3.transform(m, a) + self.trace.points[i_point]
for a in self.profile.arcs
]
normal = self.trace.tangents[i_point]
for i_arc in reversed(range(n_arc)):
vertex_buffer.add_vertex(arcs[i_arc], normal, self.color,
self.trace.objids[i_point])
